$(document).ready(function() {
/* We do not change the Disqus API. If you want to pass options to * Disqus, do it like they expect: by setting global variables. */
disqus_shortname ="example";
disqus_identifier ="/path/to/slug";
$.disqus();
});

Caveats

Be aware that the Disqus embed script manipulates comments, e.g.,
changing long URLs into anchor elements (<a>) or newlines into line-break
elements (<br>).
These manipulations must be reversed for the original Markdown to parse as
the comment author intended. I have made a minor attempt to address these two
specific manipulations, but there are others that my script will not
handle correctly.

An ideal solution would essentially require rewriting the Disqus embed script
and replacing the transformation that Disqus provides. I suspect it would be
an easy change for Disqus developers with access to the source. For me, it is
too much reverse engineering to be justified.

I have not tested this script with Disqus 2012. My suspicion is that browsers
will prohibit its access to the comments within the Disqus iframe, thus
disabling it.

History

This plugin was branched off the last published version of the jQuery Disqus
plugin by Lance Pollard. Besides being broken by the time I discovered
it (likely due to changes in the Disqus API), I believe the original plugin
tried to do too much. I have made several changes:

Use a single entry point, $.disqus().

Expect Disqus configuration to occur outside the call to this plugin and
to follow the expectations documented by Disqus.